#!/usr/bin/perl
use strict;
use warnings;

use Data::Dumper;
use Modules::Utilities;
use Modules::JunctionRW;
use Modules::JunctionFilter;


my $conf_file = "conf/conf2.txt";

print "Welcome to TGAC's Junction Filter Pipeline!\n";

my $util      = Modules::Utilities->new;
   $util->read_conf_file($conf_file);
my $jrw       = Modules::JunctionRW->new($util);

#Filter based on conf params
my $filter         = Modules::JunctionFilter->new($util);
   $filter->calc_junctions($jrw->parse_sam);
   $filter->apply_filters;

print "\nJunction Filter Pipeline finished\n";
print "TIME ELAPSED: " . $util->time_elapsed . " seconds.\n";
